Implications of the Major Health KOSs during the COVID-19 Pandemic - PowerPoint PPT Presentation

Implications of the Major Health KOSs during the COVID-19 Pandemic Yi Hong DeepThink Health, Inc. Marcia Zeng Kent State University NKOS Workshop 2020, Sept. 9 &10.

Outline Prompt actions of the major health KOSs 1. a) The recent efforts to eliminate ambiguities and semantic conflicts through naming of the disease b) New codes and coding guidance from major standardized health KOSs Usages of Health KOSs 2. Conclusion 3. Based on Chapter 1 & 2 of the full paper: Zeng, M. L., Y. Hong, J. Clunis, S. He, & L.P. Coladangelo. 2020. Implications of Knowledge Organization Systems for Health Information Exchange and Communication during the COVID-19 Pandemic. Data and Information Management , 4(3): 148-170. Available at https://doi.org/10.2478/dim-2020-0009 Hong & Zeng, NKOS Workshop 2020 2

Outline Prompt actions of the major health KOSs 1. a) The recent efforts to eliminate ambiguities and semantic conflicts through naming of the disease b) New codes and coding guidance from major standardized health KOSs Usages of Health KOSs 2. Conclusion 3. Hong & Zeng, NKOS Workshop 2020 3

The Problem of Information Overload "Information overload" refers to the difficulty a person can have understanding an issue and making decisions that can be caused by the presence of too much information. Toffler, 1970 Challenges during a global pandemic • News reports are from around the world; • Terms carry different meanings in different contexts; • Uncertain methods or criteria for collecting data; • Communicating across languages, regions, and cultures, • … Standardized health KOSs - increasingly play a larger and more important role in healthcare information systems to facilitate data normalization, -- which is a fundamental requirement for any subsequent data analysis, information management, and decision-making. Hong & Zeng, NKOS Workshop 2020 4

The Problem of Semantic conflicts Naming of a disease; Classifying and defining a disease. ◦ 2009 H1N1 Flu (Swine Flu) -- CDC •"swine flu" •"pig flu” •”[new] Spanish flu" • "Mexican flu" • "North American influenza" • "Influenza A virus subtype H1N1” – Wikipedia "Influenza A (H1N1)" – WHO — "Swine-Origin Influenza A H1N1 Virus" – CDC, (MeSH) — "Influenza A Virus, H1N1 Subtype" – MeSH — • Even after standardized authority control efforts, semantic conflicts can still occur through the way concepts are classified and defined. • Incorrect diagnoses and cause of death is a well-known problem with international morbidity and mortality statistics (O’Malley et al., 2005). 5 Hong & Zeng, NKOS Workshop 2020

LePan, Nicholas , 2020-03. “Visualizing the History of Pandemics” https://www.visualcapitalist.com/history-of-pandemics-deadliest Hong & Zeng, NKOS Workshop 2020 6

Three most important names to be decided • the species • the virus • the disease Image source: ICTV: Naming the 2019 Coronavirus. https://talk.ictvonline.org/ CC BY-SA 4.0 Gorbalenya, A.E., Baker, S.C., Baric, R.S. et al. The species Severe acute respiratory syndrome-related coronavirus : classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol 5, 536–544 (2020). https://doi.org/10.1038/s41564-020-0695-z ICTV = International Committee on Taxonomy of Viruses, the official body of the Virology Division of the International Union of Microbiological Societies. ICTV-CSG = The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses Hong & Zeng, NKOS Workshop 2020 7

WHO Best Practices for Naming of New Human Infectious Diseases https://www.who.int/topics/infectious_diseases/naming-new-diseases/en/ Ensuring that the name does not refer to ◦ a geographical location, ◦ an animal, ◦ an individual or group of people, while still being pronounceable and related to the disease (WHO, 2015). Establishing a name for a new disease provides a shared understanding for researchers and developers to discuss disease prevention, spread, transmissibility, severity, and treatment. Viruses are named based on their genetic structure to facilitate the development of diagnostic tests, vaccines, and medicines (WHO, 2020a). Hong & Zeng, NKOS Workshop 2020 8

Naming and Classifying by WHO and ICD-10* — 2020-01-30. ◦ WHO declared the 2019 Novel Coronavirus ( 2019-nCoV ) disease outbreak a public health emergency of international concern. — 2020-01-31. ◦ WHO Family of International Classifications (WHO-FIC) network’s Classification and Statistics Advisory Committee (CSAC) convened an emergency meeting to discuss the creation of a specific code for this new type of coronavirus. ◦ ICD-10 established a new emergency code (“U07.1, 2019-nCoV, acute respiratory disease”). — 2020-02-11. ◦ The WHO officially announced the name of the disease, COVID-19 , an acronym for “coronavirus disease 2019.” ◦ A study group of the International Committee on Taxonomy of Viruses (ICTV) christened the novel virus as “severe acute respiratory syndrome coronavirus 2,” or SARS-CoV-2 (ICTV, 2020). ◦ The ICD-10 was updated with two emergency codes: “U07.1 COVID-19, virus identified” and – *ICD-10 = International Classification of “U07.2 COVID-19, virus not identified” – Diseases 10th Hong & Zeng, NKOS Workshop 2020 9

WHO ICD-10 codes of COVID-19 Source: https://icd.who.int/browse10/2019/en#/U07 (Image captured 2020-04-26). Hong & Zeng, NKOS Workshop 2020 10

Releases of Guidelines by KOSs in March 2020 — ICD-10 — CPT (Current Procedural T erminology) — LOINC (Logical Observation Identifiers Names and Codes) — SNOMED CT (Systematized Nomenclature of Medicine – Clinical T erms) Refer to our full paper’s Table 1 ------ à https://doi.org/10.2478/dim-2020-0009 Hong & Zeng, NKOS Workshop 2020 11

NLM VSAC COVID-19 SNOMED CT Codeset [Note: This value set contains codes from the March 2020 Interim International Edition release. New approved terms for these codes will appear in the next release in September 2020. Source: https://confluence.ihtsdotools.org/display/snomed/SNOMED%2BCT%2BCoronavirus%2BContent] Hong & Zeng, NKOS Workshop 2020 12

MeSH Supplementary Concept for COVID-19 Source: https://meshb.nlm.nih.gov/record/ui?ui=C000657245 Hong & Zeng, NKOS Workshop 2020 13

Wikipedia and Wikidata entries of COVID-19 (Data collected on May 20, 2020) Wikipedia Wikidata # of "Also # of Wikipedia entry # of entries Wikidata English Matching KOS IDs scope notes Known as" in mapped (languages) Label and ID English "Identifier" • MeSH: COVID-19 Coronavirus 128 zoonotic respiratory 19 21 C000657245 disease 2019 syndrome and infectious (Q84263196) • ICD-10: U07.1 disease in humans, caused by SARS • ICD-10: U07.2 coronavirus 2 • SNOMED CT: 840539006 Coronavirus 69 Coronavirus group of related viruses 1 6 • ICD-10:B97.2 that cause diseases in (Q89469904) mammals and birds • MeSH:D017934 COVID-19 COVID-19 125 ongoing pandemic of 15 23 pandemic pandemic COVID-19 (Q81068910) Severe acute 102 • ICD-10: U07.1 SARS-CoV-2 strain of virus causing the 16 14 respiratory ongoing pandemic of • MeSH: syndrome (Q82069695) coronavirus disease 2019 C000656484 coronavirus 2 (COVID-19) • SNOMED CT: 840533007 Hong & Zeng, NKOS Workshop 2020 14

Outline 1. Prompt actions of the major health KOSs a) The recent efforts to eliminate ambiguities and semantic conflicts through naming of the disease b) New codes and coding guidance from major standardized health KOSs 2. Usages of Health KOSs 3. Conclusion Hong & Zeng, NKOS Workshop 2020

Common Health KOS Standards — Most popular KOS standards in EHR and HIE: v International Classification of Diseases (ICD) v Current Procedural T erminology (CPT) v SNOMED Clinical Terms (SMOMED-CT) v Logical Observation Identifiers Names and Codes (LOINC) v RxNorm v Health Lever Seven (HL7) messages Hong & Zeng, NKOS Workshop 2020

Standard health KOSs in electronic health records (EHR) Hong & Zeng, NKOS Workshop 2020

Source: https://ope nehr.org/c km/templa tes/1013.2 6.272/orgc hart COVID-19 encounter diagnosis in OpenEMR’s Problem List Source: https://www.open- emr.org/wiki/index.php/OpenE MR_Features Hong & Zeng, NKOS Workshop 2020 18

SNOMED CT code of COVID-19 Source: https://browser.ihtsdotools.org/?pers pective=full&conceptId1=840539006 &edition=MAIN/2020-07- Hong & Zeng, NKOS Workshop 2020 19 31&release=&languages=en

COVID-19 Data Exchange on the AIMS Platform Source: https://www.aphl.org/aboutAPHL/publications/Documents/INFO-2020- Hong & Zeng, NKOS Workshop 2020 20 AIMS-COVID-19-Data-Flow-Infographic.pdf

COVID-19 HL7 data messaging - Sample HL7 messages for lab data exchange LOINC code and name SNOMED CT code and name LOINC code and name Source: https://www.aphl.org/programs/preparedness/Crisis- Hong & Zeng, NKOS Workshop 2020 Management/Documents/2019nCoV_PHLIPsample_2.3.1_Detected_UPDATED3.3.20.pd f

Sample HL7 Message with “Not Detected” Test Results 2019nCoV_PHLIPsample_2.5.1_NotDetect ed_UPDATED3.3.2020 Source: https://www.aphl.org/programs/preparedness/Crisis- Hong & Zeng, NKOS Workshop 2020 Management/Documents/2019nCoV_PHLIPsample_2.5.1_NotDetected_UPDATED3.3.2020.pdf